Documentation ¶
Overview ¶
Package saint reads and parses SAINT-related files.
Index ¶
- type BaitDatRow
- type InterDatRow
- type PreyDatRow
- type Row
- type SAINT
- func (saint *SAINT) FilterByBaitNumber(minimumBaits int)
- func (s *SAINT) FilterByFDR(fdr float64)
- func (s *SAINT) GetUniProtMapping() map[string]string
- func (s *SAINT) LengthNormalizeSpectralCounts()
- func (s *SAINT) ParseInteractors(fdr float64) map[string][]string
- func (s *SAINT) SortByPreyRank(field string) map[string][]string
Constants ¶
This section is empty.
Variables ¶
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Functions ¶
This section is empty.
Types ¶
type BaitDatRow ¶
type BaitDatRow struct { ID string Name string Control bool Type string // This is for an optional 4th column that I can add to the file. }
BaitDatRow defines the headers in a bait.dat file.
type InterDatRow ¶
InterDatRow defines the headers in a bait.dat file.
type PreyDatRow ¶
PreyDatRow defines the headers in a bait.dat file.
type Row ¶
type Row struct { Bait string Prey string PreyGene string Spec []float64 AvgSpec float64 Control []float64 AvgP float64 FoldChange float64 FDR float64 NormalizedSpec float64 PreySequenceLength int }
Row defines the headers in a SAINT file.
type SAINT ¶
type SAINT []Row
SAINT is an array of Rows from a SAINT file.
func (*SAINT) FilterByBaitNumber ¶
FilterByBaitNumber filters a SAINT file by a minimum bait number required per prey.
func (*SAINT) FilterByFDR ¶
FilterByFDR removes preys not passing an FDR.
func (*SAINT) GetUniProtMapping ¶
GetUniProtMapping creates a map from UniProt accessions to gene names using the Refseq "Prey" column IDs.
func (*SAINT) LengthNormalizeSpectralCounts ¶
func (s *SAINT) LengthNormalizeSpectralCounts()
LengthNormalizeSpectralCounts substracts control counts from the average spectral count and then multiplies by the median prey length for the bait / current prey length.
func (*SAINT) ParseInteractors ¶
ParseInteractors returns significant interactors for each bait.